How to sub-sample .bam file to target coverage?
I have .bam files for blood samples from which I extract signals. Let’s assume my samples have a 30x coverage and my signal of interest is nicely detectable. To see how well the signal is detectable with lower coverage samples, I want to downsample to 20x, 10x, etc. Is there an easy way to do this?
So far I had a closer look at samtools view -s, but it takes only the target fraction and not a target coverage. Is there a program that lets me specify the target coverage that generalizes well for multiple samples with different start coverage?
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